X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreModels.java;h=7262fb81925396f1ee4ce0dd5198a68f6de8ff53;hb=e1cb1f4ff4ae05504c806d99395358629c807956;hp=2419997633123242e2417e8931c48050f2f4c844;hpb=67428050d76de7946d96d43ba16ee02d439026bd;p=jalview.git
diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java
index 2419997..7262fb8 100644
--- a/src/jalview/analysis/scoremodels/ScoreModels.java
+++ b/src/jalview/analysis/scoremodels/ScoreModels.java
@@ -1,5 +1,26 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis.scoremodels;
+import jalview.api.AlignmentViewPanel;
import jalview.api.analysis.ScoreModelI;
import jalview.io.DataSourceType;
import jalview.io.FileParse;
@@ -18,6 +39,8 @@ public class ScoreModels
private final ScoreMatrix PAM250;
+ private final ScoreMatrix DNA;
+
private static ScoreModels instance = new ScoreModels();
private Map models;
@@ -33,10 +56,9 @@ public class ScoreModels
*
* - BLOSUM62
* - PAM250
- * - SeqSpace (identity matrix)
+ * - PID
* - DNA
* - Sequence Feature Similarity
- * - Percentage Identity
*
*/
private ScoreModels()
@@ -47,10 +69,9 @@ public class ScoreModels
models = new LinkedHashMap();
BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
- loadScoreMatrix("scoreModel/dna.scm");
- loadScoreMatrix("scoreModel/seqspace.scm");
- registerScoreModel(new FeatureScoreModel());
- registerScoreModel(new PIDScoreModel());
+ registerScoreModel(new PIDModel());
+ DNA = loadScoreMatrix("scoreModel/dna.scm");
+ registerScoreModel(new FeatureDistanceModel());
}
/**
@@ -67,14 +88,15 @@ public class ScoreModels
/*
* delegate parsing to ScoreMatrixFile
*/
- FileParse fp = new FileParse(resourcePath, DataSourceType.CLASSLOADER);
+ FileParse fp = new FileParse(resourcePath,
+ DataSourceType.CLASSLOADER);
ScoreMatrix sm = new ScoreMatrixFile(fp).parseMatrix();
registerScoreModel(sm);
return sm;
} catch (IOException e)
{
- System.err.println("Error reading " + resourcePath + ": "
- + e.getMessage());
+ System.err.println(
+ "Error reading " + resourcePath + ": " + e.getMessage());
}
return null;
}
@@ -90,9 +112,20 @@ public class ScoreModels
return models.values();
}
- public ScoreModelI forName(String s)
+ /**
+ * Returns an instance of a score model for the given name. If the model is of
+ * 'view dependent' type (e.g. feature similarity), instantiates a new
+ * instance configured for the given view. Otherwise returns a cached instance
+ * of the score model.
+ *
+ * @param name
+ * @param avp
+ * @return
+ */
+ public ScoreModelI getScoreModel(String name, AlignmentViewPanel avp)
{
- return models.get(s);
+ ScoreModelI model = models.get(name);
+ return model == null ? null : model.getInstance(avp);
}
public void registerScoreModel(ScoreModelI sm)
@@ -112,10 +145,9 @@ public class ScoreModels
* @param forPeptide
* @return
*/
- public PairwiseSeqScoreModel getDefaultModel(boolean forPeptide)
+ public ScoreMatrix getDefaultModel(boolean forPeptide)
{
- return (PairwiseSeqScoreModel) (forPeptide ? forName("BLOSUM62")
- : forName("DNA"));
+ return forPeptide ? BLOSUM62 : DNA;
}
public ScoreMatrix getBlosum62()